The pearl bracelet arrived in May 2014, in the spring of Ali Watkins’ senior year in college, a graduation gift from a man many years her senior. It was the sort of bauble that might imply something more deeply felt than friendship — but then again, might not.

Watkins, then a 22-year-old intern in the Washington bureau of McClatchy Newspapers, was not entirely surprised. She had met James Wolfe, a 50-something senior aide to the Senate Intelligence Committee, while hunting for scoops on Capitol Hill. He had become a helpful source, but there were times when he seemed interested in other pursuits — like when he presented her with a Valentine’s Day card.

On that occasion, Watkins explained to Wolfe that their relationship was strictly professional. The bracelet suggested that her message had not gotten through. She asked an editor for advice, and was told that as long as the gift was not exorbitant it was fine.

Watkins kept the bracelet.

A screenshot of Ali Watkinsâ Twitter profile.Screengrab/Twitter

The story of what happened next — of a three-year affair that unfolded between a young reporter and a government official with access to top-secret information — is part of a federal investigation that has rattled the world of Washington journalists and the sources they rely on.

Wolfe, 57, was arrested June 7 and charged with lying to investigators about his contacts with Watkins and three other journalists. Watkins, a Washington-based reporter for The New York Times, had her email and phone records seized by federal prosecutors.

Now 26, Watkins was hired by The Times to cover federal law enforcement in December, about four months after she has said her relationship with Wolfe ended. Times officials are examining her work history and what influence the relationship may have had on her reporting. The Times is also reviewing her decision, on advice of her personal lawyer, not to immediately tell her editors about a letter she received in February informing her that her records had been seized.

The seizure of Watkins’ records was alarming to First Amendment advocates. With no allegation that classified information was disclosed, they said such a rare and aggressive tactic was unjustified and could undermine journalists’ ability to report on government misconduct.

Pedestrians pass in front of The New York Times Co. headquarters in New York, U.S., on Tuesday, Oct.18, 2011.Michael Nagle/Bloomberg

“The most important issue here remains the seizure of a journalist’s personal communications, which we condemn and believe all Americans should be deeply concerned about,” said Eileen Murphy, a spokeswoman for The Times.

Strikingly, the case against Wolfe brings together several of President Donald Trump’s preoccupations: leaks, which he has railed about since taking office; Washington’s bureaucracy, which he derides as the “deep state”; the news media, Trump’s favorite target; and the investigation into his campaign’s ties to Russia. The president tweeted his satisfaction that the FBI had arrested “a very important leaker,” prompting Wolfe’s lawyers to protest that their client was charged with lying, not leaking, and that he has pleaded not guilty.

This account is based on interviews with about three dozen friends and colleagues of Watkins and Wolfe, many of whom asked for anonymity to speak candidly about sensitive matters. Watkins declined to speak on the record, but she has shared many details of her experiences with others who spoke with The Times. Wolfe’s lawyers declined to comment in detail, saying: “Mr. Wolfe is fighting the charges against him in court, not in the newspaper.”

Wolfe, who is married but whose wife now lives in Connecticut, retired quietly in December, shortly after investigators questioned him about possible leaks.

Avoiding conflicts of interest is a basic tenet of journalism, and intimate involvement with a source is considered verboten. In her short career, Watkins disclosed her relationship with Wolfe to her employers in varying degrees of detail — sometimes citing Wolfe’s name and position, and sometimes not — while asserting that she had not used him as a source during their relationship.

James Wolfe, left, former director of security with the Senate Intelligence Committee accompanied by his attorney Benjamin Klubes leaves the federal courthouse, Wednesday, June 13, 2018, in Washington.Jose Luis Magana/AP

If the romance with Wolfe raised any red flags, they were not enough to prevent several news organizations from hiring Watkins, or to persuade her editors to move her off the intelligence beat. Since meeting Wolfe in 2013, Watkins reported on the Senate Intelligence Committee for Politico, BuzzFeed News, The Huffington Post and McClatchy, where her reporting was part of a submission that was a Pulitzer Prize finalist.

In May 2017, Watkins joined Politico, while she and Wolfe were still together. She has told friends that when she was hired, she informed a Politico editor, Paul Volpe, that she was dating a man in the intelligence community, though she again did not volunteer Wolfe’s name or his position.

On June 2, 2017, a shaken Watkins approached her Politico editors with a bizarre tale.

The day before, she explained, she had received an anonymous email from a man who claimed to work for the government and wanted to meet. Over drinks, the man quizzed Watkins about her sources on a story about Russian espionage. He then stunned her by reciting the itinerary of her recent vacation to Spain.

He also knew with whom she had travelled: Wolfe.

The man said he had temporarily relocated to Washington to work on leak investigations, and asked Watkins to help him identify government officials who were leaking to the press. “It would turn your world upside down” if this turned up in The Washington Post, the man said to Watkins, who told her editors she believed he was threatening to expose her personal relationship.

Watkins later went back to the bar and obtained a receipt with the man’s name on it: Jeffrey A. Rambo, a Customs and Border Protection agent stationed in California.

Two former Justice Department officials said there was a surge last year in government personnel assigned to hunt for leaks — a priority of the Trump White House — but a current official said there is no evidence Rambo was ever detailed to the FBI.

Rambo, reached by phone, declined to comment. A Border Protection spokesman said the matter has been referred to the agency’s Office of Professional Responsibility.

Inside Politico, there was curiosity over why a Border Patrol agent appeared to be targeting one of its reporters. But editors were also surprised to learn that the man Watkins had been dating was a powerful official on a committee she covered.

If Politico editors had reservations about Watkins’ relationship with Wolfe, they were not reflected in her assignments: over the following six months, she continued to write about the work of the Senate Intelligence Committee.

The most important issue here remains the seizure of a journalist's personal communications, which we condemn and believe all Americans should be deeply concerned about

By August, Watkins told friends that she and Wolfe had broken up. He had been spooked by her meeting with Rambo and was refusing to disclose their relationship to his own employers in the Senate

In December, before she started work at The Times, Watkins told the paper’s national security editor, Amy Fiscus, about her previous relationships with staff members of the Senate committee, and about her encounter with Rambo. Fiscus relayed the information to the paper’s Washington bureau chief, Elisabeth Bumiller.

Fiscus and Bumiller said in interviews that they did not feel her past relationships should be a barrier to hiring her, because Watkins said Wolfe had not been a source during their relationship, and because she would not be covering the Senate Intelligence Committee.

On Dec. 14, days before her start date, Watkins was approached by two FBI agents with questions about Wolfe, a conversation she immediately reported to her editors in the Times Washington bureau. In February, however, Watkins received a letter she did not tell her editors about: a notice from the Justice Department informing her that investigators had seized some of her email and phone records.

Obtaining a reporter’s private communications is so unusual that it is often reported as news, and media organizations generally protest such actions. But on the advice of her lawyer, Watkins kept the information to herself. She did not tell The Times until nearly four months later, when a story by her colleagues about Wolfe’s arrest was imminent; in a statement at the time, Murphy, the Times spokeswoman, said the paper “obviously would have preferred to know.”

The Times declined to comment on its internal review. Since Wolfe’s arrest, the accuracy of Watkins’ articles for The Times and other publications has not been challenged. In recent days, she has been out of the office on a preplanned vacation.